In his tweet, however, Rowghani seems to be announcing his departure from Twitter.

Re/Code foreshadowed the announcement Wednesday when the report said newly hired product VP Daniel Graf would answer directly to CEO Dick Costolo, even though Rowghani oversaw product since last fall.

Costolo responded to Rowghani's tweet shortly after he announced his leave.

Ali Rowghani, Chief Operating Officer of Twitter, resigned his position on Thursday with a tweet.JEON HEON-KYUN / EPA

"Thank you for being an incredible executive & partner," Costolo tweeted to Rowghani. "Twitter could not have succeeded without you."

Members of Twitter's management team will take on his operating responsibilities, according to the SEC filing.

The company did not say why he stepped down, but Re/Code said growth at Twitter has been lackluster, as well as product innovation under Rowghani. The report cited sources as saying these problems also included a recent large stock sale by Rowghani.

Since its $14.2 billion IPO last November the company's stock rose to a high of $74, but has fallen this year and is currently around $36. The company is up 3.3 percent in Thursday morning trading since the announcement.